Preheat oven to 350 degrees. In a medium saucepan, bring quinoa and 1 cup water to a boil. Reduce to a simmer; cover, and cook until water has been absorbed and quinoa is tender, 11 to 13 minutes.
Meanwhile, line a standard 12-cup muffin pan. In a medium bowl, whisk together flour, baking powder, salt, pumpkin spice, cinnamon, and 2 cups cooked quinoa; reserve any leftover quinoa for another use.
In a medium bowl, whisk together applesauce, almond milk, pumpkin purée, agave syrup, and vanilla. Add milk mixture to flour mixture, and stir just until combined; divide batter among prepared muffin cups.
Bake until toothpick inserted into the center of a muffin comes out clean, 25 to 35 minutes. Cool muffins in pan, 5 minutes; transfer to a wire rack to cool completely.